MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 425 to 474 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
213	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Subtracted	237.302	212.41	24.892
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Divided	210.693	186.95	1.127
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		191.644	170.192	1.12605
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Subtracted	241.282	266.12	24.838
215	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		237.292	212.457	24.835
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Divided	112	126	1.125
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Subtracted	226.471	201.769	24.702
217	60s ribosomal protein l26. [swissprot;acc:q02877]		242.326	267.008	24.682
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Divided	112	126	1.125
218	60s ribosomal protein l35. [swissprot;acc:p42766]	Subtracted	242.333	266.999	24.666
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Divided	112	126	1.125
219	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Subtracted	242.339	266.986	24.647
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Divided	112	126	1.125
220	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Subtracted	242.339	266.986	24.647
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	112	126	1.125
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Subtracted	242.627	267.151	24.524
222	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		242.153	266.673	24.52
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Divided	112	126	1.125
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Subtracted	242.153	266.673	24.52
224	60s ribosomal protein l34. [swissprot;acc:p49207]
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Divided	185.969	165.623	1.12285
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Subtracted	242.153	266.673	24.52
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]		239.991	269.238	1.12187
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Subtracted	242.153	266.673	24.52
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]		244.126	268.604	24.478
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	239.99	269.234	1.12186
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Subtracted	244.126	268.604	24.478
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Divided	226.411	202.088	1.12036
229	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Subtracted	242.195	266.663	24.468
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	226.401	202.094	1.12028
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		239.35	267.915	1.11934
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Subtracted	242.694	267.017	24.323
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Divided	239.336	267.881	1.11927
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Subtracted	226.411	202.088	24.323
232	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]		226.401	202.094	24.307
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Divided	239.336	267.879	1.11926
233	60s ribosomal protein l7. [swissprot;acc:p18124]	Subtracted	235.727	259.984	24.257
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Divided	239.32	267.842	1.11918
234	40s ribosomal protein s23. [swissprot;acc:p39028]	Subtracted	243.944	268.195	24.251
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Divided	287.41	256.835	1.11905
235	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Subtracted	243.944	268.195	24.251
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Divided	227.357	254.15	1.11785
236	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Subtracted	252.644	228.42	24.224
	pp3111 protein. [refseq;acc:nm_022156]	Divided	227.357	254.15	1.11785
237	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Subtracted	242.011	266.18	24.169
	syntaxin 18. [swissprot;acc:q9p2w9]	Divided	227.357	254.15	1.11785

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.